Haplotype tree and heatmaps

root.dir <- here::here()
knitr::opts_chunk$set(echo = TRUE, root.dir=root.dir)
knitr::opts_knit$set(root.dir = root.dir)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)

Introduction

The data/haplotype_amino.fas from haplotype analysis is used for generating haplotype tree and assessing correlation between haplotypes.

Ploting of alignement haplotypes trees

library(adegenet)
library(ips)
library(ggplot2)
library(ggtree)
library(heatmaply)

nbin<-fasta2DNAbin("data/haplotypes_AA_names.fas")
an<-as.alignment(nbin)
nm<-as.matrix(an) 
nbinmat<-as.matrix(labels(nbin))
class(nbin)
dnbin<-dist.dna(nbin, model = "K80")
tree<-njs(dnbin)
ggt<-ggtree(tree, cex = 0.8, aes(color=branch.length))+scale_color_continuous(high='lightskyblue1',low='coral4')+geom_tiplab(align=TRUE, size=5)+geom_treescale(y = -1, color = "coral4", fontsize = 7)
njmsaplot<-msaplot(ggt, nbin, offset = 0.009, width=1, height = 0.5, color = c(rep("rosybrown", 1), rep("sienna1", 1), rep("lightgoldenrod1", 1), rep("lightskyblue1", 1)))
njmsaplot

pdf("figures/haplotype_tree.pdf", width = 11, height = 9, paper = "a4", pointsize=15)#save as pdf file
njmsaplot
dev.off()

Haplotype correlation heatmaps

sat2 <- NULL
for (i in 1:nrow(nm)) {
  sat2[i] <- paste(nm[i, ], collapse="")
}

sat2 <- toupper(sat2)
sat3 <- unique(sat2)
comat = matrix(nrow=length(sat3), ncol=length(sat3))
for (i in 1:length(sat3)) { 
  si <- sat3[i]
  for (j in 1:length(sat3)) { 
    sj <- sat3[j]
    difcnt = 0
    s1 = as.vector(strsplit(as.character(si), ""))
    s2 = as.vector(strsplit(as.character(sj), ""))
    for (k in 1:length(s1[[1]])) {
      if (s1[[1]][k] != s2[[1]][k]) {
        difcnt = difcnt + 1
      }
      comat[i, j] = difcnt
      #print(paste(i, " ", j, " ", difcnt))
    }
  }
}
#comat  is Hamming distance matrix
colnames(comat)<-nbinmat

heatmap<-heatmaply_cor(cor(comat), file= "figures/heatmap.pdf",  xlab= "haplotypes", ylab="haplotypes",
              k_col=3,
              k_row=3, margins =c(10,10,15), fontsize_row = 8,
              fontsize_col = 8)

heatmap

Figures are available haplotypes_trees and Haplotype_correlations

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